biogems.info - gems for bioinformatics

New: CloudBioLinux packages are now listed on biogems.info !

#	biogem	description	by	version	released	stars	issues	total	90d*)	7d	90d**)
								downloads		commits
1	bio	Bioinformatics library (...)	BioRuby project	1.4.3.0001	14 months	30	17	66716	1441	0	0
2	biodiversity	Parser of scientific names (...)	Dmitry Mozzherin	3.1.4	7 months	14	5	37014	690	0	0
3	bio gem	Biogem is a software generator for Ruby in (...)	Raoul J.P. Bonnal, Pjotr Prins	1.3.6	10 weeks	14	11	30391	478	0	3
4	simple spreadsheet extractor	Basic spreadsheet content extraction using apache poi (...)	Stuart Owen, Finn Bacall	0.13.3	4 months	4	1	30294	870	0	0
5	bio samtools	Binder of samtools for Ruby, on the top (...)	Ricardo Ramirez-Gonzalez, Dan MacLean, Raoul J.P. Bonnal	2.0.5	8 weeks	17	5	25076	620	0	57
6	t2 server	Support for interacting with taverna 2 server (...)	Robert Haines, Finn Bacall	1.1.0	3 months	2	...	20426	696	0	139
7	entrez	Http requests to entrez e-utilities (...)	Jared Ning	0.5.8.1	2 years	4	...	19177	255	0	0
8	bio ucsc api	The Ruby ucsc api: accessing the ucsc genome (...)	Hiroyuki Mishima, Jan Aerts	0.6.2	4 months	13	1	19121	364
9	bio gadget	Gadgets for bioinformatics (...)	Shintaro Katayama	0.4.8	13 months		...	17028	464	0	0
10	sequenceserver	Blast search made easy! (...)	Anurag Priyam, Ben J Woodcroft, Yannick Wurm	0.8.7	6 months	30	30	15813	257	2	51
11	bio gff3	Gff3 parser for big data (...)	Pjotr Prins	0.9.1	23 months	6	2	15292	209	0	0
12	taverna t2flow	Support for interacting with taverna 2 workflows (...)	Finn Bacall, Robert Haines, David Withers et al.	0.5.1	4 months		...	14783	670
13	bio maf	Maf parser for BioRuby (...)	Clayton Wheeler	1.0.1	24 months	10	30	13573	270	0	0
14	search biomodel	Interfaces with biomodel search engine (...)	Niall Beard	2.1.6	2 years		...	12962	180	0	0
15	bio svgenes	Create pretty svg-format images of features, gene models (...)	Dan MacLean	0.4.1	6 months	7	5	11596	450
16	bio grid	A biogem to submit jobs on a queue (...)	Francesco Strozzi	0.3.3	21 months	5	...	11561	256	0	0
17	bio logger	Log4r wrapper with extra features for roles and (...)	Pjotr Prins	1.0.1	2 years	4	2	11194	148	0	0
18	bio blastxmlparser	Very fast blast xml parser and library for (...)	Pjotr Prins	1.1.1	17 months	9	...	9108	161	0	0
19	bio faster	A fast parser for fastq files (...)	Francesco Strozzi	0.4.5	2 years	9	...	8750	154	0	0
20	bio alignment	Support for multiple sequence alignments (msa) (...)	Pjotr Prins	0.0.8	11 weeks	6	4	8465	175	0	0
21	bio table	Swiss army knife of tabulated data; transforming/filtering tab/csv (...)	Pjotr Prins	1.0.0	8 weeks	7	20	7831	201	0	14
22	bio phyta	Pipeline to remove contaminations from est libraries (...)	Philipp Comans	0.9.4	2 years	1	1	7623	107	0	0
23	bio dbla classifier	A tool to classify and manipulate pfemp1 dbl-alpha (...)	George Githinji	0.7.1	17 months	1	...	7380	116	0	0
24	scaffolder	Build genome output files (...)	Michael Barton	0.5.0	11 months	3	...	7032	82	0	0
25	bio bigbio	Low memory sequence emitters (...)	Pjotr Prins	0.1.6	10 weeks	8	1	6961	141	0	9
26	bio assembly	BioRuby assembly plugin (...)	Chase Miller, Francesco Strozzi	0.1.0	3 years	4	...	6762	78	0	0
27	bio signalp	A wrapper for the signal peptide prediction algorith (...)	Ben J Woodcroft	0.3.0	23 months	1	...	6272	101	0	0
28	bio nexml	BioRuby plugin for reading and writing nexml (http://nexml.org) (...)	Rutger Vos, Anurag Priyam	1.1.0	2 years	7	1	6259	84	0	0
29	eutils	Lightweight Ruby api for ncbi eutils (...)	Joon Lee, aka seouri	0.2.1	13 months	6	...	6197	83
30	genfrag	This is a development release (...)	Pjotr Prins and Trevor Wennblom	0.0.0.4	4 years			6180	54
31	bio tm hmm	A BioRuby plugin for interaction with the transmembrane (...)	Ben J. Woodcroft	0.2.2	20 months	2	...	6177	107	0	0
32	bio isoelectric point	A BioRuby plugin for calculating the isoelectric point (...)	George Githinji, Pascal Betz	0.1.3	2 years	3	...	6047	91
33	biointerchange	An open source framework for transforming heterogeneous data (...)	Joachim Baran, Kevin B. Cohen, Geraint Duck et al.	1.0.1	11 months	8	3	6030	167	3	13
34	bio band	Data mining algorithms for jRuby (...)	arrigonialberto86	0.1.11	10 months	14	3	5952	226	0	0
35	bio sambamba	Ruby wrapper for sambamba tool (...)	Artem Tarasov	0.0.5	23 months	2	...	5854	102	0	0
36	bio graphics	Library for visualizing genomic regions (...)	Jan Aerts	1.4	6 years			5852	66
37	bio kmer counter	A biogem for counting small kmers for fingerprinting (...)	Ben J Woodcroft	0.1.2	14 months	5	...	5633	126
38	bio genomic interval	A BioRuby plugin: handling genomic interavals and overlaps (...)	Hiroyuki Mishima	0.1.2	3 years	4	...	5622	74
39	bio ngs	Bio-ngs provides a framework for handling ngs data (...)	Francesco Strozzi, Raoul J.P. Bonnal	0.5.2	2 years	29	14	5394	63	0	0
40	bio octopus	Running and parsing of the protein transmembrane domain (...)	Ben J Woodcroft	0.1.1	3 years	1	...	5174	67	0	0
41	goruby	Gene ontology (go) interface for Ruby (...)	Ben J Woodcroft	0.2.0	3 years	8	...	4540	45	0	0
42	bio bwa	Ruby binding for bwa mapping software (...)	Francesco Strozzi	0.2.2	3 years	4	...	4452	69	0	0
43	bio bgzf	Reading/writing bgzf blocks (...)	Artem Tarasov, Clayton Wheeler	0.2.1	24 months	2	...	4378	92	0	0
44	ruby ensembl api	Api to ensembl databases (...)	Jan Aerts, Francesco Strozzi	1.0.1	3 years	30	4	4292	33	0	0
45	bio lazyblastxml	A plugin that allows you to parse large (...)	robsyme	0.4.0	3 years	1	...	4262	68	0	0
46	bio pileup iterator	Iterate through a samtools pileup file (...)	Ben J. Woodcroft	0.0.4	20 months	2	...	4081	63
47	bio cd hit report	Read and manipulate cd-hit clusters (...)	George Githinji	0.1.0	15 months	2	1	3752	88
48	bio kb illumina	Geneexpression illuminahumanannotation (...)	Raoul J.P. Bonnal	0.1.0	3 years	1	...	3454	43
49	bio tabix	Ruby binding for samtools tabix (...)	throwern	1.0.1	10 months	3	...	3451	98	0	0
50	bio plasmoap	Implementation of the plasmoap algorithm (...)	Ben J Woodcroft	0.0.2	2 years	1	...	3428	43	0	0
51	bio gff3 pltools	Ruby wrapper for the gff3-pltools (...)	Marjan Povolni	0.3.0	24 months			3256	68
52	taverna baclava	Ruby support for the baclava file format (...)	Robert Haines	1.0.1	4 months	1	...	3212	526	0	0
53	bio chembl	Chembl rest api client, parser and container (...)	Mitsuteru Nakao	0.1.3	2 years	1	1	3187	66
54	bio ucsc util	Ruby binding to the ucsc kent utilities (...)	throwern	0.1.2	22 months	2	...	3176	70
55	bio gngm	Next-generation mapping of mutations (...)	Dan MacLean	0.2.1	20 months	2	...	3162	65	0	0
56	bio rdf	Bioinformatics triple-store support (...)	Pjotr Prins	0.0.2	2 years	4	1	3138	47	20	77
57	bio affy	Parse affymetrix cel/cdf files (...)	Pjotr Prins	0.5.1	2 years	2	1	3087	42	0	0
58	bio basespace sdk	Basespace Ruby sdk is a Ruby based software (...)	Joachim Baran, Raoul Bonnal, Eri Kibukawa et al.	0.1.7	11 months	10	2	3044	120
59	bio core	BioRuby core plugins, most and stable plugins. blastxmlparser, (...)	Raoul J.P. Bonnal	0.0.1	2 years	1	...	2910	45
60	bio cnls screenscraper	Programmatic interface to the cnls nuclear localisation signal (...)	Ben J. Woodcroft	0.3.0	2 years	1	...	2728	45	0	0
61	bio wolf psort wrapper	Enables the localisation predictor wolf psort to be (...)	Ben J Woodcroft	0.0.3	2 years	1	...	2678	45	0	0
62	bio unichem	BioRuby plugin for unichem rest web service (...)	Mitsuteru Nakao	0.3.0	17 months		...	2412	67
63	taverna player	Taverna player is a rails plugin to run (...)	Robert Haines	0.8.0	5 weeks	4	...	2395	138	0	11
64	bio hmmer model	Parse pfam hmm definition files (...)	Ben J. Woodcroft	0.0.2	2 years	1	...	2339	40
65	bio synreport	Reports whether a nucleotide change results in synonymous (...)	Dan MacLean	0.1.2	14 months		...	2292	66	0	0
66	bio protparam	A protparam compatible utility for BioRuby (...)	hryk	0.2.0	19 months	1	...	2283	45
67	bio krona	This biogem is built around krona, a flashy (...)	Ben J. Woodcroft	0.1.1	11 months	1	...	2256	70	0	0
68	bio statsample timeseries	Timeseries modules for statsample (...)	Ankur Goel, Claudio Bustos	0.2.1	10 months		...	2252	94
69	bio gag	Bio-gag is a biogem for detecting and correcting (...)	Ben J Woodcroft	0.1.0	21 months	2	...	2189	47	0	0
70	bio sge	BioRuby plugin for sun grid engine (...)	Toshiaki Katayama	0.0.0	3 years	4	...	1799	22	0	0
71	bio hello	Hello world plugin for the BioRuby (just for (...)	Toshiaki Katayama	0.0.0	3 years	3	...	1784	21
72	bio restriction enzyme	Digests dna based on restriction enzyme cut patterns (...)	Trevor Wennblom	1.0.0	2 years		1	1780	20
73	bioportal	Supports linking of models within a ror application (...)	Stuart Owen, Quyen Nguyen	2.2	4 months		...	1754	519	0	0
74	dna sequence aligner	Does high pairwise alignment of sequencing reads with (...)	John T. Prince	0.0.2	4 years	1	...	1730	14
75	publisci	Publish scientific results to the semantic web (...)	Will Strinz	0.1.6	7 weeks	3	16	1712	99	0	3
76	bio velvet	Parser to work with file formats used in (...)	Ben J Woodcroft	0.4.2	2 weeks		...	1548	251
77	bio emboss six frame nucleotide sequences	A method to get the nucleotide sequence of (...)	Ben J Woodcroft	0.1.0	3 years	1	...	1526	24	0	0
78	bio core ext	BioRuby core ext: plugins which require external library (...)	Raoul J.P. Bonnal, Pjotr Prins	0.0.1	2 years	1	...	1525	25	0	0
79	bio data restriction enzyme	Restriction enzyme dataset (...)	Sir Richard J. Roberts, Trevor Wennblom	1.109.0	2 years		...	1488	28
80	bio biolinux	Meta package for biolinux distribution (...)	Raoul J.P. Bonnal	0.1.0	2 years	2	...	1474	25	0	0
81	bio ensembl	A Ruby api to the ensembl database (...)	Jan Aerts, Francesco Strozzi	1.1.0	2 years	3	...	1469	25	0	0
82	bio foo	One-line summary of your gem (...)	Toshiaki Katayama	0.0.0	2 years	1	...	1456	25	0	0
83	bio dbsnp	Decoding the dbsnp bitfield (...)	Hiroyuki Mishima	0.1.1	2 years	2	...	1428	26
84	bio phyloxml	Phyloxml plugin for BioRuby (...)	Diana Jaunzeikare, Clayton Wheeler	0.9.0	2 years	3	...	1415	25
85	bio exportpred	Wrapper around the exportpred algorithm for predicting p (...)	Ben J Woodcroft	0.0.1	2 years	1	...	1403	22
86	bio aliphatic index	A simple biogem that allows computation of the (...)	Ben J Woodcroft	0.0.1	2 years	1	...	1384	24	0	0
87	bio hydropathy	Hydropathy scale for BioRuby (...)	Ben J Woodcroft	0.0.1	2 years	1	...	1369	24	0	0
88	bio hmmer3 report	Enables parsing of hmmer version 3 reports (...)	Christian Zmasek, Ben J Woodcroft	0.0.1	2 years	1	1	1259	24
89	intermine bio	Biological extensions for the intermine webservice client library (...)	Alex Kalderimis	0.98.1	2 years		...	1238	17	0	0
90	bio gggenome	Gggenome Ruby client (...)	Mitsuteru Nakao	0.2.0	11 months	1	...	1212	39
91	bio incanter	Build graph with jRuby (...)	Matteo Picciolini	0.1.0	24 months		...	1171	25
92	bio ipcress	A programmatic interface to the ipcress in-silico pcr (...)	Ben J Woodcroft	0.0.1	24 months	1	...	1168	23
93	bio ensembl rest	Ruby ensembl rest api (...)	Alberto Donizetti	0.2.0	10 months	3	1	1125	45
94	bio liftover	Ruby solution for ucsc liftover tool- (ucsc http://genome.ucsc.edu/cgi-bin/hgliftover) (...)	Andrei Rozanski	1.3.0	4 months		...	1085	96
95	bio statsample glm	Generalized linear models for statsample (...)	Ankur Goel	0.1.1	10 months		...	1078	47
96	bio vcf	Vcf parser (...)	Pjotr Prins	0.7.0	5 weeks	12	6	1068	119	0	181
97	bio polyploid tools	Tool to work with polyploids, ngs and molecular (...)	Ricardo H. Ramirez-Gonzalez	0.3.3	8 weeks		...	1038	122	1	23
98	bio img metadata	Reads metadata from integrated microbial genomes (img) metadata (...)	Ben J. Woodcroft	0.0.1	18 months		...	921	23
99	bio commandeer	Dead simple method of running shell commands from (...)	Ben J. Woodcroft	0.1.0	6 months		...	798	46	0	0
100	bio express beta diversity	Interface for express beta diversity (...)	Ben J. Woodcroft	0.1.0	6 months		...	770	51	0	0
101	bio repeatmasker	Bio-repeatmasker (...)	Andrei Rozanski	0.0.3	6 months			766	54
102	bio biostars analytics	Biostars data-mining and statistical analysis (...)	Joachim Baran	0.2.0	3 months		...	744	83	0	0
103	bio stockholm	Parse stockholm sequence alignment format (...)	Ben J. Woodcroft	0.0.1	13 months	2	...	706	25	0	0
104	bio raxml	Ruby wrapper to run standard-raxml for maximum likelihood (...)	Fernando Izquierdo	0.1.0	12 months		...	638	22	0	0
105	bio cigar	A parser for cigar format alignments (...)	Ben J Woodcroft	0.1.0	5 months	3	...	614	48
106	bio velvet underground	Bindings to some internals of the velvet assembler (...)	Ben Woodcroft	0.1.0	9 weeks		1	524	63	0	7
107	bio samtools server	Web server for bio-samtools (...)	homonecloco	0.1.2	8 weeks		...	462	67
108	bio qtlHD	(...) pre		pre				351	2
109	bio exominer	Mine publications for gene names (...)	Pjotr Prins	0.0.3	5 months		...	306	26	0	0
110	bio polymarker db batch	Server for polymarker. to be used with cron (...) new	Ricardo H. Ramirez-Gonzalez	0.2.1	1 week		...	304	304	0	13
111	genomichdt	A restful service for sharing genomic data (...)	Joachim Baran, Robert Buels, Michel Dumontier	0.0.1	4 months	2	...	252	21	0	0
112	bio locus	Fast storage and comparison of chr+pos(+alt) locations (...)	Pjotr Prins	0.0.2	8 weeks		...	201	39
113	bio kseq	Ruby inferface for kseq.h by heng li for (...) new	Fedor Gusev	0.0.2	2 weeks		...	117	114	0	25
114	bio primer3	(...) pre		pre				80	2

*) gem downloads (total & last 90 days) from rubygems.org as of 2014-07-31
**) number of commits on GitHub (last 7 days & last 90 days)